rs1525402

chr17-10955347-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.226 in 151,996 control chromosomes in the GnomAD database, including 4,048 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.23 (4048 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.307

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34371 AN: 151878 Hom.: 4043 Cov.: 32

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.228

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.226 AC: 34406 AN: 151996 Hom.: 4048 Cov.: 32 AF XY: 0.230 AC XY: 17109 AN XY: 74294

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.310

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.294

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.226

Alfa AF: 0.223 Hom.: 6584

Bravo AF: 0.233

Asia WGS AF: 0.215 AC: 750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.85
Dann	Benign	0.39

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1525402; hg19: chr17-10858664;